[Bioperl-l] about fgenesh result manipunation
Magic Fang
fangl at genomics.org.cn
Sun Feb 23 16:00:17 EST 2003
How to create a model to parse a genscan-liked result like below:
FGENESH 1.1 Prediction of potential genes in Homo_sapiens genomic DNA
Time : Mon Dec 9 10:11:02 2002
Seq name: QULTROPIA
Length of sequence: 5025
Number of predicted genes 1 in +chain 1 in -chain 0
Number of predicted exons 7 in +chain 7 in -chain 0
Positions of predicted genes and exons:
G Str Feature Start End Score ORF Len
1 + 1 CDSf 318 - 409 -1.01 318 - 407 90
1 + 2 CDSi 521 - 590 -0.36 522 - 590 69
1 + 3 CDSi 2962 - 3003 8.79 2962 - 3003 42
1 + 4 CDSi 3308 - 3436 8.85 3308 - 3436 129
1 + 5 CDSi 3957 - 4046 14.20 3957 - 4046 90
1 + 6 CDSi 4159 - 4335 31.57 4159 - 4335 177
1 + 7 CDSl 4659 - 4757 13.24 4659 - 4757 99
1 + PolA 4941 1.12
Predicted protein(s):
>FGENESH: 1 7 exon (s) 318 - 4757 232 aa, chain +
MHMLQAPSSQCSPRAELPLLWSCLACPSQGSQLLAACQSVLASRRGSLFLLRTRKKRRAA
TARRQHLKSAMLQLAVTEIEKEAAAKEVEKQNYLAEHCPPLSLPGSMQELQELCKKLHAK
IDSVDEERYDTEVKLQKTNKELEDLSQKLFDLRGKFKRPPLRRVRMSADAMLRALLGSKH
KVNMDLRANLKQVKKEDTEKEKDLRDVGDWRKNIEEKSGMEGRKKMFEAGES
.
I have create a model of it, the code is:
# $Id: FgeneSH.pm,v 0.1 2003/02/23 08:38:32 lapp Exp $
#
# BioPerl module for Bio::Tools::FgeneSH
#
# Cared for by Magic Fang <fangl at genomics.org.cn>
#
# Copyright Magic Fang
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::FgeneSH - Results of one FgeneSH run
=head1 SYNOPSIS
$FgeneSH = Bio::Tools::FgeneSH->new(-file => 'result.FgeneSH');
# filehandle:
$FgeneSH = Bio::Tools::FgeneSH->new( -fh => \*INPUT );
# parse the results
# note: this class is-a Bio::Tools::AnalysisResult which implements
# Bio::SeqAnalysisParserI, i.e., $FgeneSH->next_feature() is the same
while($gene = $FgeneSH->next_prediction()) {
# $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
# off Bio::SeqFeature::Gene::Transcript.
#
# $gene->exons() returns an array of
# Bio::Tools::Prediction::Exon objects
# all exons:
@exon_arr = $gene->exons();
# initial exons only
@init_exons = $gene->exons('Initial');
# internal exons only
@intrl_exons = $gene->exons('Internal');
# terminal exons only
@term_exons = $gene->exons('Terminal');
# singleton exons:
($single_exon) = $gene->exons();
}
# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$FgeneSH->close();
=head1 DESCRIPTION
The FgeneSH module provides a parser for FgeneSH gene structure prediction
output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript-
derived object.
This module also implements the Bio::SeqAnalysisParserI interface, and thus
can be used wherever such an object fits. See L<Bio::SeqAnalysisParserI>.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs at bio.perl.org
http://bio.perl.org/bioperl-bugs/
=head1 AUTHOR - Magic Fang
Email fangl at genomics.org.cn
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::FgeneSH;
use vars qw(@ISA);
use strict;
use Symbol;
use Bio::Root::Root;
use Bio::Tools::AnalysisResult;
use Bio::Tools::Prediction::Gene;
use Bio::Tools::Prediction::Exon;
@ISA = qw(Bio::Tools::AnalysisResult);
sub _initialize_state {
my ($self, at args) = @_;
# first call the inherited method!
$self->SUPER::_initialize_state(@args);
# our private state variables
$self->{'_preds_parsed'} = 0;
$self->{'_has_cds'} = 0;
# array of pre-parsed predictions
$self->{'_preds'} = [];
# seq stack
$self->{'_seqstack'} = [];
}
=head2 analysis_method
Usage : $FgeneSH->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/FgeneSH/i.
Returns : String
Argument : n/a
=cut
#-------------
sub analysis_method {
#-------------
my ($self, $method) = @_;
if($method && ($method !~ /FgeneSH/i)) {
$self->throw("method $method not supported in " . ref($self));
}
return $self->SUPER::analysis_method($method);
}
=head2 next_feature
Title : next_feature
Usage : while($gene = $FgeneSH->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the FgeneSH result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
=cut
sub next_feature {
my ($self, at args) = @_;
# even though next_prediction doesn't expect any args (and this method
# does neither), we pass on args in order to be prepared if this changes
# ever
return $self->next_prediction(@args);
}
=head2 next_prediction
Title : next_prediction
Usage : while($gene = $FgeneSH->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the FgeneSH result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
=cut
sub next_prediction {
my ($self) = @_;
my $gene;
# if the prediction section hasn't been parsed yet, we do this now
$self->_parse_predictions() unless $self->_predictions_parsed();
# get next gene structure
$gene = $self->_prediction();
if($gene) {
# fill in predicted protein, and if available the predicted CDS
#
my ($id, $seq);
# use the seq stack if there's a seq on it
my $seqobj = pop(@{$self->{'_seqstack'}});
if(! $seqobj) {
# otherwise read from input stream
($id, $seq) = $self->_read_fasta_seq();
# there may be no sequence at all, or none any more
if($id && $seq) {
$seqobj = Bio::PrimarySeq->new('-seq' => $seq,
'-display_id' => $id,
'-alphabet' => "protein");
}
}
if($seqobj) {
# check that prediction number matches the prediction number
# indicated in the sequence id (there may be incomplete gene
# predictions that contain only signals with no associated protein
# and CDS, like promoters, poly-A sites etc)
$gene->primary_tag() =~ /^>FgeneSH:\s+([0-9]+)\s+\.+$/;
my $prednr = $1;
if($seqobj->display_id() !~ /^>FgeneSH:\s+$prednr\s+\.+$/) {
# this is not our sequence, so push back for next prediction
push(@{$self->{'_seqstack'}}, $seqobj);
} else {
$gene->predicted_protein($seqobj);
# CDS prediction, too?
if($self->_has_cds()) {
($id, $seq) = $self->_read_fasta_seq();
$seqobj = Bio::PrimarySeq->new('-seq' => $seq,
'-display_id' => $id,
'-alphabet' => "dna");
$gene->predicted_cds($seqobj);
}
}
}
}
return $gene;
}
=head2 _parse_predictions
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
=cut
sub _parse_predictions {
my ($self) = @_;
my %exontags = ('CDSf' => 'Initial',
'CDSi' => 'Internal',
'CDSl' => 'Terminal',
'CDSo' => '');
my $gene;
my $seqname;
while(defined($_ = $self->_readline())) {
if(/^\s*(\d+)\s+([\+|\-])/) {
# exon or signal
my $prednr = $1;
my $signalnr = $2; # not used presently
if(! defined($gene)) {
$gene = Bio::Tools::Prediction::Gene->new(
'-primary' => "GenePrediction$prednr",
'-source' => 'FgeneSH');
}
# split into fields
chomp();
my @flds = split(/\s+/, $_);
# create the feature object depending on the type of signal
my $predobj;
my $is_exon = grep {$_ eq $flds[4];} (keys(%exontags));
if($is_exon) {
$predobj = Bio::Tools::Prediction::Exon->new();
} else {
# PolyA site, or Promoter
$predobj = Bio::SeqFeature::Generic->new();
}
# set common fields
$predobj->source_tag('FgeneSH');
$predobj->score($flds[$#flds]);
$predobj->strand((($flds[2] eq '+') ? 1 : -1));
# add to gene structure (should be done only when start and end
# are set, in order to allow for proper expansion of the range)
if($is_exon) {
# first, set fields unique to exons
$predobj->start($flds[5]);
$predobj->end($flds[7]);
$predobj->start_signal_score(0);
$predobj->end_signal_score(0);
$predobj->coding_signal_score($flds[8]);
$predobj->significance($flds[8]);
$predobj->primary_tag($exontags{$flds[4]} . 'Exon');
$predobj->is_coding(1);
# Figure out the frame of this exon. This is NOT the frame
# given by FgeneSH, which is the absolute frame of the base
# starting the first predicted complete codon. By comparing
# to the absolute frame of the first base we can compute the
# offset of the first complete codon to the first base of the
# exon, which determines the frame of the exon.
my $cod_offset;
if($predobj->strand() == 1) {
$cod_offset = $flds[9] - $predobj->start();
# Possible values are -2, -1, 0, 1, 2. -1 and -2 correspond
# to offsets 2 and 1, resp. Offset 3 is the same as 0.
} else {
# On the reverse strand the FgeneSH frame also refers to
# the first base of the first complete codon, but viewed
# from forward, which is the third base viewed from
# reverse.
$cod_offset = $flds[10] - $predobj->end();
}
# Offsets 2 and 1 correspond to frame 1 and 2 (frame of exon
# is the frame of the first base relative to the exon, or the
# number of bases the first codon is missing).
$predobj->frame($cod_offset);
# then add to gene structure object
$gene->add_exon($predobj, $exontags{$flds[4]});
} else {
$predobj->start($flds[4]);
$predobj->end($flds[4]);
if($flds[3] eq 'PolA') {
$predobj->primary_tag("PolyAsite");
$gene->poly_A_site($predobj);
} elsif($flds[3] eq 'TSS') {
$predobj->primary_tag("Promoter");
$gene->add_promoter($predobj);
}
}
next;
}
if(/^\s*$/ && defined($gene)) {
# current gene is completed
$gene->seq_id($seqname);
$self->_add_prediction($gene);
$gene = undef;
next;
}
if(/^\s+(FgeneSH)\s+(\S+) Prediction of potential genes in (\S+) genomic DNA/i) {
$self->analysis_method($1);
$self->analysis_method_version($2);
$self->analysis_subject($3);
next;
}
if(/^\s+Seq name\:\s+(\S+)/i) {
$seqname = $1;
next;
}
if(/^Predicted coding/) {
$self->_has_cds(1);
next;
}
/^>/ && do {
# section of predicted sequences
$self->_pushback($_);
last;
};
}
$self->_predictions_parsed(1);
}
=head2 _prediction
Title : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
=cut
sub _prediction {
my ($self) = @_;
return undef unless(exists($self->{'_preds'}) && @{$self->{'_preds'}});
return shift(@{$self->{'_preds'}});
}
=head2 _add_prediction
Title : _add_prediction()
Usage : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :
=cut
sub _add_prediction {
my ($self, $gene) = @_;
if(! exists($self->{'_preds'})) {
$self->{'_preds'} = [];
}
push(@{$self->{'_preds'}}, $gene);
}
=head2 _predictions_parsed
Title : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
=cut
sub _predictions_parsed {
my ($self, $val) = @_;
$self->{'_preds_parsed'} = $val if $val;
if(! exists($self->{'_preds_parsed'})) {
$self->{'_preds_parsed'} = 0;
}
return $self->{'_preds_parsed'};
}
=head2 _has_cds
Title : _has_cds()
Usage : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE
=cut
sub _has_cds {
my ($self, $val) = @_;
$self->{'_has_cds'} = $val if $val;
if(! exists($self->{'_has_cds'})) {
$self->{'_has_cds'} = 0;
}
return $self->{'_has_cds'};
}
=head2 _read_fasta_seq
Title : _read_fasta_seq()
Usage : ($id,$seqstr) = $obj->_read_fasta_seq();
Function: Simple but specialised FASTA format sequence reader. Uses
$self->_readline() to retrieve input, and is able to strip off
the traling description lines.
Example :
Returns : An array of two elements.
=cut
sub _read_fasta_seq {
my ($self) = @_;
my ($id, $seq);
local $/ = ">";
my $entry = $self->_readline();
if($entry) {
$entry =~ s/^>//;
# complete the entry if the first line came from a pushback buffer
while($entry !~ />$/) {
last unless $_ = $self->_readline();
$entry .= $_;
}
# delete everything onwards from an intervening empty line (at the
# end there might be statistics stuff)
$entry =~ s/\n\n.*$//s;
# id and sequence
if($entry =~ /^(\S+)\n([^>]+)/) {
$id = $1;
$seq = $2;
} else {
$self->throw("Can't parse FgeneSH predicted sequence entry");
}
$seq =~ s/\s//g; # Remove whitespace
}
return ($id, $seq);
}
1;
but every time return a error like:
------------- EXCEPTION -------------
MSG: Can't parse FgeneSH predicted sequence entry
STACK Bio::Tools::FgeneSH::_read_fasta_seq /usr/lib/perl5/site_perl/5.6.1/Bio/Tools/FgeneSH.pm:475
STACK Bio::Tools::FgeneSH::next_prediction /usr/lib/perl5/site_perl/5.6.1/Bio/Tools/FgeneSH.pm:202
STACK toplevel /home/fangl/perl/fgenesh2blat.pl:38
--------------------------------------
Can anybody tell me why?
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